Methods and compounds for polynucleotide synthesis

Abstract

Methods of forming polynucleotides are disclosed.

1. A method of forming polynucleotides, comprising:
 providing a structure X selected from 
 
       
         
           
           
               
               
           
         
         where R1 is selected from oxycarbonate, aryl ester, alkyl ester, alkyl silane, aryl silane, alkylsiloxane, arylsiloxane, alkylarylsilane, and alkylarylsiloxane and functional groups, where the functional group is selected from carbonate, ester, amide, carbamate, silane, siloxane, orthoester, acetal, and ketal; 
         where R2 is selected from benzyl, alkylbenzyl, dialkylbenzyl, trialkylbenzyl, thioalkylbenzyl, phenylthiobenzyl, dithioalkylbenzyl, trithioalkylbenzyl, thioalkylhalobenzyl, alkyloxybenzyl, dialkyloxybenzyl, halobenzyl, dihalobenzyl, trihalobenzyl, and esterified salicyl; 
         where B is optionally a purine or pyrimidine base or analog thereof; 
         wherein n is from 1 to 350; and 
         wherein ● is a substrate; and 
         oxidizing and deprotecting structure X simultaneously in an aqueous buffer solution, wherein the aqueous buffer solution comprises an oxidant and a nucleophile at a pH of about 6to 10. 
       
     
     
       2. The method of  claim 1 , wherein the aqueous buffer solution is selected from hydrogen peroxide, peracids, performic acid, peracetic acid, perbenzoic acid, chloroperbenzoic acid, hydroperoxides, butylhydroperoxide, benzylhydroperoxide, phenylhydroperoxide, and combinations thereof. 
     
     
       3. The method of  claim 1 , wherein the aqueous buffer solution comprises hydrogen peroxide. 
     
     
       4. The method of  claim 1 , wherein R1 is selected from oxycarbonate, aryl ester, alkyl ester, alkyl silane, aryl silane, alkylsiloxane, arylsiloxane, alkylarylsilane, and alkylarylsiloxane, and wherein R2 is selected from alkylbenzyl, dialkylbenzyl, trialkylbenzyl, thioalkylbenzyl, phenylthiobenzyl, dithioalkylbenzyl, trithioalkylbenzyl, thioalkylhalobenzyl, alkyloxybenzyl, dialkyloxybenzyl, halobenzyl, dihalobenzyl, trihalobenzyl, and esterified salicyl. 
     
     
       5. The method of  claim 1 , wherein the pH of the aqueous buffer solution is about 6.5 to 8.5. 
     
     
       6. The method of  claim 1 , wherein the pH of the aqueous buffer solution is about 6.5 to 8. 
     
     
       7. The method of  claim 1 , wherein the pH of the aqueous buffer solution is about 7 to 8. 
     
     
       8. The method of  claim 1 , wherein oxidizing and deprotecting is an irreversible process. 
     
     
       9. The method of  claim 1 , wherein oxidizing and deprotecting produces a product selected from: 
       
         
           
           
               
               
           
         
         wherein n is from 2 to 350.